Demonstration of scRNA-seq analysis workflow

scRNAseq: Bioconductor

DropletUtils: Bioconductor

scater: Bioconductor, GitHub, Paper

ggbeeswarm: CRAN, GitHub

Demo Dataset: BachMammaryData from Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing Nat Commun. 2017;8(1):2128.

License: GPL-3.0

Introduction

we will use the example data set BachMammaryData from the scRNAseq Bioconductor package to demonstrate how to use various R packages, such as scater, DropletUtils, ggplot2, etc to perform scRNA-seq analysis.

This mouse scRNA-seq dataset contains expression values of mammary epithelial cells of 8 samples (G_1, G_2, L_1, L_2, NP_1, NP_2, PI_1, PI_2) from four developmental time points; nulliparous (NP), day 14.5 gestation (G), day 6 lactation (L) and 11 days post natural involution (PI).

Prerequisites

Demo Data

Install the scRNAseq package and follow the steps in Part 1 to load BachMammaryData.

R Packages

# From CRAN
install.packages(c("scales", "ggbeeswarm"))

# From Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("scRNAseq", "DropletUtils", "scater"))

Resources

Maintained by I-Hsuan Lin
License: GNU General Public License v3.0